A few simple math function for other Oxford Nanopore processing scripts
Project description
# nanomath
This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
[](https://twitter.com/wouter_decoster) [](https://anaconda.org/bioconda/nanomath) [](https://tracker.debian.org/pkg/python-nanomath)
## FUNCTIONS
Calculate read N50 from a set of lengths get_N50(readlenghts)
Remove extreme length outliers from a dataset remove_length_outliers(dataframe, columname)
Calculate the average Phred quality of a read ave_qual(qualscores)
Write out the statistics report after calling readstats function write_stats(dataframe, outputname)
Compute a number of statistics, return a dictionary calc_read_stats(dataframe)
As of v1.3.0, nanomath calculates the average quality differently, by first converting per-read phred scale averages to error rates, take the average, and converting back ([nanostat#40](<https://github.com/wdecoster/nanostat/issues/40>))
## INSTALLATION
`bash pip install nanomath `
or [](https://anaconda.org/bioconda/nanomath)
` conda install -c bioconda nanomath `
## CONTRIBUTORS
[@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
## CITATION
If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
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](https://twitter.com/wouter_decoster){kind=link}
](https://anaconda.org/bioconda/nanomath){kind=link}
](https://tracker.debian.org/pkg/python-nanomath){kind=link}